SUMMARY DUF1220 protein domains have undergone the largest human lineage-specific increase in copy number of any protein coding region in the genome (~290 copies in human haploid genome), and map primarily to 1q21, a region where copy number variations containing many DUF1220 copies have been repeatedly linked to autism, schizophrenia, micro- and macrocephaly. DUF1220 copy number exhibits a broad Gaussian distribution in human populations, and is a rich source of unexamined functional allelic variation. Previously we have implicated DUF1220 copy number (dosage) in human brain expansion and normal and pathological changes in brain size. Over the past year we have demonstrated that DUF1220 (CON1 subtype) dosage is linearly associated with increasing symptom severity of autism (now confirmed by a replication study) and also inversely with schizophrenia severity and risk. These findings are remarkable in that they imply that dosage variations within the same protein domain family (DUF1220) may be involved in human brain evolution, autism and schizophrenia, and that these processes may be genetically and mechanistically interrelated. Building on these significant findings, we will expand our study of DUF1220 copy number in autism and schizophrenia severity (Aim 1) and risk (Aim 2) and in micro-/macrocephaly (Aim 3) using methods we have used successfully (ddPCR, 1q21-targeted arrayCGH) as well as through application of novel methods that have the potential to significantly improve DUF1220 copy number analysis (Aim 4). For example, we have recently optimized and validated our sequence read-depth method for measuring DUF1220 copy number at high resolution and precision from whole genome sequence (WGS) data. We will apply this approach to WGS data from 1) the Autism 10K project in collaboration with Dr. Stephen Scherer, and 2) to several additional large WGS datasets that are emerging for autism and schizophrenia. In addition, we have established a subcontract with our collaborator, Dr. Pui Kwok, to apply Irys, an optical mapping method for automated genome mapping of long (>150kb) single DNA molecules, to assess DUF1220 copy number variation in these disorders. The Irys approach should be aided by our development of a CRISPR-Cas9 method which allows DUF1220-specific labeling of genomic DNA. These approaches, including our exploration of long-read sequencing technologies, will be facilitated by utilization of a new, more accurate and gap-free 1q21 assembly we recently helped generate. Finally, we will build on our recent progress linking DUF1220 function to increases in neuron number by testing whether DUF1220 promotes neural stem cell (H9-derived) proliferation in a dosage-dependent manner and identifying cellular pathways affected by progressively increasing DUF1220 dosage.